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ipqb bootcamp programming assignment
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from __future__ import division, print_function | |
import sys | |
if sys.version_info[0] < 3: | |
print("Python 3 required") | |
sys.exit(1) | |
import math, urllib.request, re | |
try: | |
import matplotlib.pyplot as plt | |
import seaborn as sns | |
except ImportError: | |
print("Requires matplotlib and seaborn for plotting") | |
sys.exit(1) | |
def dot(a, b): | |
return sum([p*q for p, q in zip(a, b)]) | |
def add(a, b): | |
return [p+q for p, q in zip(a, b)] | |
def sub(a, b): | |
return [p-q for p, q in zip(a, b)] | |
def norm(a): | |
length = math.sqrt(sum([p**2 for p in a])) | |
return [p/length for p in a] | |
def cross(a, b): | |
return [a[1]*b[2] - a[2]*b[1], a[2]*b[0] - a[0]*b[2], | |
a[0]*b[1] - a[1]*b[0]] | |
if __name__ == "__main__": | |
try: | |
pdb_id = sys.argv[1] | |
except IndexError as e: | |
print("Requires PDB id") | |
regex = r"ATOM\s*\d*\s*([CA|N]*)\s*([A-Z]{3})\s[A-Z]\s*([-0-9]*)\s*([-0-9,\.]*)\s*([-0-9,\.]*)\s*([0-9,\.]*)" | |
regex = re.compile(regex, re.MULTILINE) | |
url = "http://www.rcsb.org/pdb/files/%s.pdb"%pdb_id | |
response = "".join(urllib.request.urlopen(url).read().decode("utf-8").split("\n")) | |
atom_types, res_names, pos, xs, ys, zs = zip(*re.findall(regex, response)) | |
num_residues = len(atom_types)//3 | |
coords = list(zip(map(float, xs), map(float, ys), map(float, zs))) | |
assert len(atom_types)%3 is 0, "Some residues may be missing backbone atoms" | |
angles = [[], []] | |
for angle_idx, angle_offset in enumerate([2, 0]): | |
for res_pos in range(len(atom_types)//3 - 1): | |
atom_set = [coords[res_pos*3+angle_offset-3+j] for j in range(4)] | |
b1, b2, b3 = (sub(atom_set[i], atom_set[i+1]) for i in range(3)) | |
n1, n2 = norm(cross(b1, b2)), norm(cross(b2, b3)) | |
x = dot(n1, n2) | |
y = dot(cross(n1, norm(b2)), n2) | |
angles[angle_idx].append(math.degrees(math.atan2(y, x))) | |
sns.set_style("whitegrid") | |
plt.title(pdb_id) | |
plt.axes().set_aspect("equal") | |
plt.xticks([-180, -90, 0, 90, 180]) | |
plt.yticks([-180, -90, 0, 90, 180]) | |
plt.scatter(*angles, color=sns.color_palette()[0]) | |
plt.xlim((-180, 180)) | |
plt.ylim((-180, 180)) | |
sns.axlabel(r"$\phi$", r"$\psi$") | |
plt.savefig("%s.png"%pdb_id) | |
print("Saved Ramachandran plot to %s.png in the current working directory"%pdb_id) |
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